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Crystal structure D196N mutant of monoglyceride lipase from bacillus sp. H257 in complex with 1-rac-lauroyl glycerol
Analyse Crystal structure D196N mutant of monoglyceride lipase from bacillus sp. H257… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KE6
- Type
- protein
- Length
- 1,417 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable monoacylglycerol lipase
- EC
- 3.1.1.23
- UniProt
- P82597
- Ligands
- 1QW
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 247 | 38% helix, 19% strand | P82597 |
| B | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 241 | 38% helix, 18% strand | P82597 |
| C | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 239 | 38% helix, 18% strand | P82597 |
| D | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 237 | 36% helix, 19% strand | P82597 |
| E | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 226 | 40% helix, 17% strand | P82597 |
| F | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 227 | 40% helix, 17% strand | P82597 |
Ligands and binding sites
- 1QW · (2R)-2,3-dihydroxypropyl dodecanoate · ligand · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.82 | 0.83 | 95 | 1QW, MPD |
| 2 | 340 | 0.72 | 0.84 | 38 | empty |
| 3 | 252 | 0.72 | 0.86 | 32 | empty |
| 4 | 222 | 0.62 | 0.81 | 27 | empty |
| 5 | 458 | 0.61 | 0.76 | 34 | empty |
Interfaces
5 interfaces between chains.
- C–F · 854 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 829 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 812 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 514 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 153 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4KE6 · Crystal structure D196N mutant of Monoglyceride lipase from Bacillus sp. H257 in complex… · the same entry in another collection · chain F against F, TM-score 1.00
- P82597 · AlphaFold monomer V2.0 prediction for thermostable monoacylglycerol lipase (P82597) · a predicted model of the same protein · chain E against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P82597
- Elsewhere: RCSB PDB 4KE6 · PDBe 4KE6 · UniProt P82597
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